From 89030f8ea96b93a89638959336691eecfd28fa90 Mon Sep 17 00:00:00 2001
From: asetGem <amandine.perrin@pasteur.fr>
Date: Mon, 9 Nov 2020 15:23:05 +0100
Subject: [PATCH] Default is iqtree2. if iqtree1, specify it
---
PanACoTA/subcommands/tree.py | 30 +++++++++++++----------
PanACoTA/tree_module/iqtree_func.py | 32 ++++++++++++++++---------
test/test_unit/test_tree/test_iqtree.py | 11 +++++----
3 files changed, 45 insertions(+), 28 deletions(-)
diff --git a/PanACoTA/subcommands/tree.py b/PanACoTA/subcommands/tree.py
index b0d24abe..d4a0a06e 100755
--- a/PanACoTA/subcommands/tree.py
+++ b/PanACoTA/subcommands/tree.py
@@ -116,18 +116,22 @@ def main(cmd, align, outdir, soft, model, threads, boot=False, write_boot=False,
print("quicktree is not installed. 'PanACoTA tree' cannot run.")
sys.exit(1)
from PanACoTA.tree_module import quicktree_func as tree
- elif soft == "iqtree":
- if not utils.check_installed("iqtree"): # pragma: no cover
- if not utils.check_installed("iqtree2"):
- print("IQtree is not installed. 'PanACoTA tree' cannot run.")
- sys.exit(1)
- else:
- soft == "iqtree2"
- from PanACoTA.tree_module import iqtree_func as tree
elif soft == "iqtree2":
+ # by default, iqtree2 (not iqtree).
+ # So, if user did not specify, it means iqtree2. But if 'iqtree2' command
+ # does not exist, use iqtree command instead.
# test if iqtree2 is installed and in the path
if not utils.check_installed("iqtree2"): # pragma: no cover
- print("iqtree2 is not installed. 'PanACoTA tree' cannot run.")
+ if not utils.check_installed("iqtree"):
+ print("IQtree2 is not installed. 'PanACoTA tree' cannot run.")
+ sys.exit(1)
+ else:
+ soft == "iqtree"
+ from PanACoTA.tree_module import iqtree_func as tree
+ elif soft == "iqtree":
+ # user specifically asked for iqtree (version 1)
+ if not utils.check_installed("iqtree"): # pragma: no cover
+ print("IQtree is not installed. 'PanACoTA tree' cannot run.")
sys.exit(1)
from PanACoTA.tree_module import iqtree_func as tree
@@ -179,11 +183,13 @@ def build_parser(parser):
help=("Directory where tree results will be saved. "))
# Choose with which soft inferring phylogenetic tree
- softparse = parser.add_argument_group('Choose soft to use (default is IQtree)')
+ softparse = parser.add_argument_group('Choose soft to use (default is IQtree2)')
softs = ["fasttree", "fastme", "quicktree", "iqtree", "iqtree2"]
- softparse.add_argument("-s", "--soft", dest="soft", choices=softs, default="iqtree",
+ softparse.add_argument("-s", "--soft", dest="soft", choices=softs, default="iqtree2",
help=("Choose with which software you want to infer the "
- "phylogenetic tree. Default is IQtree."))
+ "phylogenetic tree. Default is IQtree2 "
+ "(versions 2.x of IQtree). If you want version 1.x of "
+ "IQtree, use '-s iqtree'"))
optional = parser.add_argument_group('Optional arguments')
optional.add_argument("-b", "--boot", dest="boot", type=int,
diff --git a/PanACoTA/tree_module/iqtree_func.py b/PanACoTA/tree_module/iqtree_func.py
index 980f0ab6..282d9ada 100644
--- a/PanACoTA/tree_module/iqtree_func.py
+++ b/PanACoTA/tree_module/iqtree_func.py
@@ -91,17 +91,27 @@ def run_tree(alignfile, boot, outdir, quiet, threads, **kwargs):
mem_info = ""
threadinfo = ""
- # Get info on all options
- if boot and soft=="iqtree":
- bootinfo = f"-bb {boot}"
- elif boot:
- bootinfo = f"-B {boot}"
- if write_boot and soft == "iqtree":
- wb_info = "-wbt"
- elif write_boot:
- wb_info = "--boot-trees"
+ # Get info on all options (syntax changes according to IQtree version 1.x or 2.x)
+ if boot:
+ if soft=="iqtree":
+ bootinfo = f"-bb {boot}"
+ else:
+ bootinfo = f"-B {boot}"
+ if write_boot:
+ if soft == "iqtree":
+ wb_info = "-wbt"
+ else:
+ wb_info = "--boot-trees"
if memory:
- mem_info = f"-mem {memory}"
+ if soft=="iqtree":
+ mem_info = f"-mem {memory}"
+ else:
+ mem_info = f"--mem {memory}"
+ # IQtree is always run quietly, but syntax depends on version:
+ if soft=="iqtree":
+ qu = "-quiet"
+ else:
+ qu = "--quiet"
# Get threads information
if threads:
if soft == "iqtree":
@@ -125,7 +135,7 @@ def run_tree(alignfile, boot, outdir, quiet, threads, **kwargs):
else:
prefix = f"--prefix {treefile}"
cmd = (f"{soft} -s {alignfile} {threadinfo} -m {model} {mem_info} {bootinfo} {wb_info} "
- f"{seqtype} {prefix} -quiet {fast}")
+ f"{seqtype} {prefix} {qu} {fast}")
logger.details("IQtree command: " + cmd)
if quiet:
fnull = open(os.devnull, 'w')
diff --git a/test/test_unit/test_tree/test_iqtree.py b/test/test_unit/test_tree/test_iqtree.py
index aec93da4..993c7920 100644
--- a/test/test_unit/test_tree/test_iqtree.py
+++ b/test/test_unit/test_tree/test_iqtree.py
@@ -99,7 +99,7 @@ def test_run_iqtree2_default(caplog):
assert ("iqtree2 -s test/data/align/exp_files/exp_pers4genomes.grp.aln "
"-T 1 -m GTR --seqtype DNA "
"--prefix test/data/tree/generated_by_unit-tests/exp_pers4genomes.grp.aln.iqtree_tree "
- "-quiet") in caplog.text
+ "--quiet") in caplog.text
assert tutil.is_tree_lengths(treefile)
assert not tutil.is_tree_bootstrap(treefile)
@@ -183,7 +183,7 @@ def test_run_iqtree2_boot_write_boot(caplog):
assert ("iqtree2 -s test/data/align/exp_files/exp_pers4genomes.grp.aln "
"-T 1 -m GTR -B 1000 --boot-trees --seqtype DNA "
"--prefix test/data/tree/generated_by_unit-tests/exp_pers4genomes.grp.aln.iqtree_tree "
- "-quiet") in caplog.text
+ "--quiet") in caplog.text
assert not tutil.is_tree_lengths(treefile)
assert tutil.is_tree_bootstrap(treefile)
@@ -236,9 +236,10 @@ def test_run_iqtree2_fast_mem_quiet(caplog):
logs = os.path.join(GENEPATH, "exp_pers4genomes.grp.aln.iqtree_tree.log")
assert os.path.isfile(logs)
assert "Running IQtree..." in caplog.text
- assert ("iqtree2 -s test/data/align/exp_files/exp_pers4genomes.grp.aln "
- "-T 1 -m GTR -mem 4GB --seqtype DNA "
+ assert ("iqtree2 -s test/data/align/exp_files/exp_pers4genomes.grp.aln -T 1 "
+ "-m GTR --mem 4GB --seqtype DNA "
"--prefix test/data/tree/generated_by_unit-tests/exp_pers4genomes.grp.aln.iqtree_tree "
- "-quiet -fast") in caplog.text
+ "--quiet -fast") in caplog.text
assert tutil.is_tree_lengths(treefile)
assert not tutil.is_tree_bootstrap(treefile)
+
--
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